Add taxon constraints

[rays22]

This commit intends to

1. add taxon constraint in taxon some Arthropoda to some terms
   using a ROBOT template,
2. add taxon restriction annotation never in taxon Mammalia (NCBITaxon:40674) to some terms using another ROBOT template.

If applied, this commit will address #2050.

Notes

• I had to delete the following 2 terms from the ROBOT template, because they cause OBO format multiple name tags not allowed errors:

UBERON:6003006  adult segment   owl:Class   ('in taxon' some Arthropoda)
UBERON:6000154  embryonic segment   owl:Class   ('in taxon' some Arthropoda)

• I also had to delete the following term from the ROBOT template, because it appears to be obsolete and raises validation errors:

UBERON:6000000  embryonic germ layer derivative owl:Class   ('in taxon' some Arthropoda)

[paolaroncaglia]

@rays22
I see that checks have failed :-(

[dosumis]

I had to delete the following 2 terms from the ROBOT template, because they cause OBO format multiple name tags not allowed errors

Assume your template doesn't add labels?

[paolaroncaglia]

@rays22 @matentzn

I had to delete the following 2 terms from the ROBOT template, because they cause OBO format multiple name tags not allowed errors:
UBERON:6003006 adult segment owl:Class ('in taxon' some Arthropoda)
UBERON:6000154 embryonic segment owl:Class ('in taxon' some Arthropoda)

Looking into this, the current version of Uberon (not the slim!) has
UBERON:6003006 insect adult segment
UBERON:6000154 insect embryonic segment
I think Chris changed those after Nico produced the slim, so now Uberon and slim are out of synch; could that be the problem? There are no labels 'adult segment' or 'embryonic segment' in Uberon.

[paolaroncaglia]

As a reminder, the ROBOT templates should be applied to Uberon, not to the slim, right?

[paolaroncaglia]

Because we'd want taxon rules applied upstream.

[dosumis]

@rays22 - fail is presumably due to inconsistencies triggered by adding taxon constraints. This is a good thing as it will allow us to clean things up. Please paste a sample inconsistency report from robot (See other PR for how to do this) or Protege. Happy to help debug. Could meet briefly to discuss if you're still stuck. But not until tomorrow.

[rays22]

I had to delete the following 2 terms from the ROBOT template, because they cause OBO format multiple name tags not allowed errors

Assume your template doesn't add labels?

Apparently it does... :(

I can add these terms with another template, but first I need to check the QC errors.

[rays22]

% sh run.sh make tmp/materialized.owl
% tail -100 tmp/materialized.owl.LOG | pbcopy
2021-10-19 11:00:42,579 ERROR org.obolibrary.robot.ReasonerHelper - There are 11 unsatisfiable classes in the ontology.
2021-10-19 11:00:42,580 ERROR org.obolibrary.robot.ReasonerHelper -     unsatisfiable: http://purl.obolibrary.org/obo/UBERON_0007260
2021-10-19 11:00:42,581 ERROR org.obolibrary.robot.ReasonerHelper -     unsatisfiable: http://purl.obolibrary.org/obo/UBERON_0015853
2021-10-19 11:00:42,582 ERROR org.obolibrary.robot.ReasonerHelper -     unsatisfiable: http://purl.obolibrary.org/obo/UBERON_0007261
2021-10-19 11:00:42,583 ERROR org.obolibrary.robot.ReasonerHelper -     unsatisfiable: http://purl.obolibrary.org/obo/UBERON_0015852
2021-10-19 11:00:42,583 ERROR org.obolibrary.robot.ReasonerHelper -     unsatisfiable: http://purl.obolibrary.org/obo/UBERON_0016622
2021-10-19 11:00:42,585 ERROR org.obolibrary.robot.ReasonerHelper -     unsatisfiable: http://purl.obolibrary.org/obo/UBERON_0007262
2021-10-19 11:00:42,585 ERROR org.obolibrary.robot.ReasonerHelper -     unsatisfiable: http://purl.obolibrary.org/obo/UBERON_0007263
2021-10-19 11:00:42,586 ERROR org.obolibrary.robot.ReasonerHelper -     unsatisfiable: http://purl.obolibrary.org/obo/UBERON_0007264
2021-10-19 11:00:42,587 ERROR org.obolibrary.robot.ReasonerHelper -     unsatisfiable: http://purl.obolibrary.org/obo/UBERON_0007265
2021-10-19 11:00:42,588 ERROR org.obolibrary.robot.ReasonerHelper -     unsatisfiable: http://purl.obolibrary.org/obo/UBERON_0005083
2021-10-19 11:00:42,588 ERROR org.obolibrary.robot.ReasonerHelper -     unsatisfiable: http://purl.obolibrary.org/obo/UBERON_0003910

[dosumis]

Assume your template doesn't add labels?

Apparently it does... :(

Please switch all templates to just 2 columns - SUBJECT and OBJECT

Please paste a sample inconsistency report from robot (See other PR for how to do this) or Protege

Sorry - should have been clearer. We need some inconsistency explanations. Nico added something on how to do this with Robot. In Protege Click the question mark on inferred subClassOf Nothing - present on inconsistent terms.

[rays22]

Please, see the report attached to #2108 for the inconsistencies.

@rays22 - fail is presumably due to inconsistencies triggered by adding taxon constraints. This is a good thing as it will allow us to clean things up. Please paste a sample inconsistency report from robot (See other PR for how to do this) or Protege. Happy to help debug. Could meet briefly to discuss if you're still stuck. But not until tomorrow.